Package org.biojava.bio.seq

Class LazyFeatureHolder

java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.seq.LazyFeatureHolder
All Implemented Interfaces:
FeatureHolder, Changeable
public abstract class LazyFeatureHolder extends AbstractChangeable implements FeatureHolder
Wrapper implementation of FeatureHolder which calls a method to create a contained FeatureHolder on demand. This is an abstract class and is normally used like: FeatureHolder fh = new LazyFeatureHolder() { protected FeatureHolder createFeatureHolder() { SimpleFeatureHolder features = new SimpleFeatureHolder(); // Create some features in here... return features; } } ;
Since:
1.2
Author:
Thomas Down, Matthew Pocock
See Also:

  • Constructor Details

    • LazyFeatureHolder

      protected LazyFeatureHolder()
      Construct a LazyFeatureHolder with the schema of its contained featureholder

    • LazyFeatureHolder

      protected LazyFeatureHolder(FeatureFilter schema)
      Construct a LazyFeatureHolder with the specified schema

  • Method Details

    • getSchema

      public FeatureFilter getSchema()
      Description copied from interface: FeatureHolder
      Return a schema-filter for this FeatureHolder. This is a filter which all Features immediately contained by this FeatureHolder will match. It need not directly match their child features, but it can (and should!) provide information about them using FeatureFilter.OnlyChildren filters. In cases where there is no feature hierarchy, this can be indicated by including FeatureFilter.leaf in the schema filter.

      For the truly non-informative case, it is possible to return FeatureFilter.all. However, it is almost always possible to provide slightly more information that this. For example, Sequence objects should, at a minimum, return FeatureFilter.top_level. Feature objects should, as a minimum, return FeatureFilter.ByParent(new FeatureFilter.ByFeature(this)).

      Specified by:
      getSchema in interface FeatureHolder
      Returns:
      the schema filter

    • createFeatureHolder

      protected abstract FeatureHolder createFeatureHolder()

    • flushFeatures

      protected void flushFeatures()

    • features

      public Iterator features()
      Description copied from interface: FeatureHolder
      Iterate over the features in no well defined order.
      Specified by:
      features in interface FeatureHolder
      Returns:
      an Iterator

    • countFeatures

      public int countFeatures()
      Description copied from interface: FeatureHolder
      Count how many features are contained.
      Specified by:
      countFeatures in interface FeatureHolder
      Returns:
      a positive integer or zero, equal to the number of features contained

    • filter

      public FeatureHolder filter(FeatureFilter ff)
      Description copied from interface: FeatureHolder
      Query this set of features using a supplied FeatureFilter.
      Specified by:
      filter in interface FeatureHolder
      Parameters:
      ff - the FeatureFilter to apply.
      Returns:
      all features in this container which match filter.

    • filter

      public FeatureHolder filter(FeatureFilter ff, boolean recurse)
      Description copied from interface: FeatureHolder
      Return a new FeatureHolder that contains all of the children of this one that passed the filter fc. This method is scheduled for deprecation. Use the 1-arg filter instead.
      Specified by:
      filter in interface FeatureHolder
      Parameters:
      ff - the FeatureFilter to apply
      recurse - true if all features-of-features should be scanned, and a single flat collection of features returned, or false if just immediate children should be filtered.

    • createFeature

      public Feature createFeature(Feature.Template template) throws BioException, ChangeVetoException
      Description copied from interface: FeatureHolder
      Create a new Feature, and add it to this FeatureHolder. This method will generally only work on Sequences, and on some Features which have been attached to Sequences.
      Specified by:
      createFeature in interface FeatureHolder
      Throws:
      BioException - if something went wrong during creating the feature
      ChangeVetoException - if this FeatureHolder does not support creation of new features, or if the change was vetoed

    • removeFeature

      public void removeFeature(Feature f) throws ChangeVetoException, BioException
      Description copied from interface: FeatureHolder
      Remove a feature from this FeatureHolder.
      Specified by:
      removeFeature in interface FeatureHolder
      Throws:
      ChangeVetoException - if this FeatureHolder does not support feature removal or if the change was vetoed
      BioException - if there was an error removing the feature

    • containsFeature

      public boolean containsFeature(Feature f)
      Description copied from interface: FeatureHolder
      Check if the feature is present in this holder.
      Specified by:
      containsFeature in interface FeatureHolder
      Parameters:
      f - the Feature to check
      Returns:
      true if f is in this set

    • getChangeSupport

      protected ChangeSupport getChangeSupport(ChangeType ct)
      Description copied from class: AbstractChangeable
      Called to retrieve the ChangeSupport for this object.

      Your implementation of this method should have the following structure: 

       ChangeSupport cs = super.getChangeSupport(ct);

 if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
   someForwarder = new ChangeForwarder(...

   this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange);
 }

 return cs;
      It is usual for the forwarding listeners (someForwarder in this example) to be transient and lazily instantiated. Be sure to register & unregister the forwarder in the code that does the ChangeEvent handling in setter methods.
      Overrides:
      getChangeSupport in class AbstractChangeable